Summary phylogenetic tree avian influenza PB2 segment

Time-rooted Maximum clade credibility phylogenetic tree of the polymerase subunit (PB2) segment of highly pathogenic avian influenza viruses isolated from wild birds and poultry during the 2014-2015 outbreak in North America. Nodes dates are the mean posterior estimate and are annotated with phylodynamic estimates of uncertainty if posterior probability was > 0.5. NEXUS fil

Birth death multitype model initialization file, PB2 segment wild birds

xml file created from the BEAUTI template for the birth-death multi type model (https://github.com/denisekuehnert/bdmm) to implement Bayesian estimation of phylodynamic parameters in BEAST v2.4.3 (available from www.BEAST2.org) from 1 chain of 10 million iterations. Set-up for analysis of 38 aligned whole segment sequences of the polymerase subunit (PB2) gene of isolates from wild birds during the 2014-2015 highly pathogenic avian influenza HA clade 2.3.4.4 outbreak in North America

Birth death multitype model initialization file, PB2 segment

xml file created from the BEAUTI template for the birth-death multi type model (https://github.com/denisekuehnert/bdmm) to implement Bayesian estimation of phylodynamic parameters in BEAST v2.4.3 (available from www.BEAST2.org) from 1 MCMC chain of 10 million iterations. Set-up for analysis of 85 aligned whole segment sequences of the Polymerase Subunit (PB2) gene of isolates from the 2014-2015 highly pathogenic avian influenza HA clade 2.3.4.4 outbreak in North America

Summary phylogenetic tree avian influenza HA segment

Summary time-rooted Maximum clade credibility phylogenetic tree of the hemagglutinin segment of highly pathogenic avian influenza viruses isolated from wild birds and poultry during the 2014-2015 outbreak in North America. Nodes dates are the mean posterior estimate and are annotated with phylodynamic estimates of uncertainty if posterior probability was > 0.5. NEXUS fil

Birth death multitype model initialization file, HA segment

xml file created from the BEAUTI template for the birth-death multi type model (https://github.com/denisekuehnert/bdmm) to implement Bayesian estimation of phylodynamic parameters in BEAST v2.4.3 (available from www.BEAST2.org) with 1 MCMC chain of 10 million iterations. Set-up for analysis of 85 aligned whole segment sequences of the hemagglutinin (HA) gene of isolates from the 2014-2015 highly pathogenic avian influenza HA clade 2.3.4.4 outbreak in North America

Birth death multitype model initialization file, M segment wild birds

xml file created from the BEAUTI template for the birth-death multi type model (https://github.com/denisekuehnert/bdmm) to implement Bayesian estimation of phylodynamic parameters in BEAST v2.4.3 (available from www.BEAST2.org) from 1 chain of 10 million iterations. Set-up for analysis of 38 aligned whole segment sequences of the matrix (M) gene of isolates from wild birds during the 2014-2015 highly pathogenic avian influenza HA clade 2.3.4.4 outbreak in North America

Summary phylogenetic tree avian influenza M segment

Summary time-rooted Maximum clade credibility phylogenetic tree of the matrix gene (M) segment of highly pathogenic avian influenza viruses isolated from wild birds and poultry during the 2014-2015 outbreak in North America. Nodes dates are the mean posterior estimate and are annotated with phylodynamic estimates of uncertainty if posterior probability was > 0.5. NEXUS fil

Birth death multitype model initialization file, HA segment wild birds

xml file created from the BEAUTI template for the birth-death multi type model (https://github.com/denisekuehnert/bdmm) to implement Bayesian estimation of phylodynamic parameters in BEAST v2.4.3 (available from www.BEAST2.org) from 1 chain of 10 million iterations. Set-up for analysis of 38 aligned whole segment sequences of the hemagglutinin (HA) gene of isolates from wild birds during the 2014-2015 highly pathogenic avian influenza HA clade 2.3.4.4 outbreak in North America

Number of AIv RNA-positive water and fecal samples at each wetland of the California Central Valley for the three sampling periods.

a<p>For rRT-PCR result interpretation, we considered samples with a Ct value≤40.0 as AIv-positive.</p>b<p>AIv isolates include one H3N8 at SAC1 in late July, one H4N8 and two H2N3 at LDC1 in mid-August, and one H3N8 at LDC2 in mid-August in fecal samples.</p>c<p>Samples collected at a different wetland to that sampled previously.</p>d<p>Presence of cows at this wetland at sampling time.</p

Location of the study wetlands.

<p>Water and fecal samples were collected during three periods across summer at all wetlands.</p